To make myself clear, I'm aware that one of Superman's major weaknesses is magic, but is that because he's also superpowered by a yellow sun, or just because he's from Krypton? Would Kryptonians be as susceptible to magic under a red sun?
There doesn't appear to have been any suggestion that Kryptonians would be any more resistant to magic under a red sun. I can find only one reference to magic on Krypton, in Superman Vol 1 279. The linked reference doesn't give much detail, but even in the unlikely event that "Ca-Rox, a stage magician from old Krypton who actually had magical powers" used those powers to attack his fellow Kryptonians, it would have been difficult to gauge whether those attacks would have been more or less effective had those Kryptonians had been under a yellow sun.